Mitochondria analytics

Visualization and analysis tools for analyzing mitochondria in the Layer 2/3 EM volume

visualize all mitochondria in a cell of interest


Contents


Folders

classifier folder: mitochondria classifier using random forests for pyramidal neurons in the Layer 2/3 volume.

mito_to_mito_distance_statistics folder: summary statistics for mitochondria-to-mitochondria (mito centroid-to-mito centroid) used in the classifier analysis.

node_metrics folder: derivation of mitochondria segmentation node metrics (“nodeplots”).


Visualization tools

Visualize a single mitochondrion of interest in Neuroglancer

neuroglancer_link_generator_mitochondria_visualization_version.ipynb: generate a Neuroglancer link for a single cellid and single mitochondrion from the pni_mito_cellswskel_v185_fullstats.csv datatable. The view will be centered at the centroid of the mitochondrion in the volume.

neuroglancer link to a single mitochondrion with crosshair at the mito centroid


Visualize all mitochondria in a neuron of interest in Neuroglancer

neuroglancer_link_generator_all_mitochondria.ipynb: generate a Neuroglancer link for all the mitochondria in a single cellid of interest pulling the mito ids from the 211019_mitochondria_info.csv datatable.

neuroglancer link generator for all mitochondria in a cell

Visualize neuronal mitochondria by compartment in Neuroglancer

neuroglancer_link_generator_neuronalmitochondria_bycompartment.ipynb: as above, but allows to select for a compartment of interest. Neuronal compartment assignments are based on the method described by Reconstruction of neocortex: Organelles, compartments, cells, circuits, and activity Turner et al, Cell 2022.

neuroglancer link generator for mitochondria by compartment

3D visualizer of all mitochondria in a cell of interesting using Meshparty, vtk, and OpenGL viewer

vtk_mitochondria_visualizer.ipynb: generate a 3D interactive view of all mitochondria in a cell of interest. Note this method has significant file download and space requirements compared to using the Neuroglancer viewer.

3D visualizer of all mitochondria in a cell

3D visualizer of all mitochondria and synapses in a cell of interesting using Meshparty, vtk, and OpenGL viewer

vtk_mitochondria_visualizer_with_synapses.ipynb: generate a 3D interactive view of all mitochondria in a cell of interest along with the pre- and post-syanptic sites. Note this method has significant file download and space requirements compared to using the Neuroglancer viewer.

3D visualizer of all mitochondria and synapses in a cell

3D vector plots by cellid lookup by neuronal subtype

mitochondria_3d_vector_plots_by_cellid_lookup_by_neuronal_subtype.ipynb: generate 3D interactive scatterplots in Plotly, 3D quiver plots in matplotlib, and a Neuroglancer views with this notebook. Uses a dataframe that generates spatial and vector calculations from the original mitochondria dataframe by Turner et al. Download mito_above_soma.csv in the data folder.

3D quiver plot of mito centroid with bounding box distance vector

3D visualization for mitochondria within a 45 degree cone above soma

3dvisualizer_for_withincone.ipynb: generate 3D interactive scatterplots in Plotly, 3D quiver plots in matplotlib, and Neuroglancer views with this notebook. Uses a dataframe that generates spatial, vector, and cone angle calculations from the original mitochondria dataframe by Turner et al. Download pyr_all.csv in the data folder. Special thanks to Qiao Liu and Wanwen Zeng at Stanford for their assistance in debugging the code.

3D scatterplot using Plotly for visualizing mitochondria within a 45 degree cone above soma

Nodeplot for mitochondria segmentation node metrics

Example nodeplot (nodeid vs. nodedist by compartment color) for pyramidal neuron cellid 648518346349537297. This example shows that certain mitochondria where the compartment is unidentified could potentially be inferred from the mitochondria node metrics data. See also node_metrics folder for additional details.

matplotlib scatterplot of nodeid vs. nodedist by compartment color from mitochondria segmentation node metrics